Stacy - Thanks for your thoughts. The transition has been all positive for us. I did a quick comparison of the whole milk that I buy and DDs formula and, on a calorie-for-calorie basis, found that the whole milk actually has more fat and protein and just slightly less carbs than her formula (and carbs are pretty easy to supplement in her diet for us). With her intake up, she's getting even more fat and protein and comparable carbs. However, your point is well taken about the other vitamins and nutrients in formula. I'm going to all her doc and get a recommendation/perscription for vitamins for her to take.
She's pretty much dropped the "bedtime" bottle so I'm going to let that one go and I think I'll switch to a sippy cup for her daytime bottle since we have to make the transition for daycare anyway. Plus she can drink on it (with water) on and off all day, and I think I'll keep the breakfast bottle cuz it works very well in our day and I can get some cuddles while she drinks it.